use more portable /usr/bin/env perl for scripts

cd-hit-2d-para.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 # =============================================================================
 # CD-HIT
 # http://cd-hit.org/
@@ -11,6 +11,7 @@
 #                                      Email liwz@sdsc.edu
 # =============================================================================
 
+use warnings;
 use strict;
 no strict "refs";
 

cd-hit-auxtools/cd-hit-dup-PE-out.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my $script_name = $0;
 my $script_dir = $0;

cd-hit-div.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #not like cd-hit-div, this script do not sort input
 #or throw away seq

cd-hit-para.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 # =============================================================================
 # CD-HIT
 # http://cd-hit.org/
@@ -11,6 +11,7 @@
 #                                      Email liwz@sdsc.edu
 # =============================================================================
 
+use warnings;
 use strict;
 no strict "refs";
 

clstr2tree.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 $clstr = shift;
 $fr = shift; # for nr80.clstr $fr = 0.8

clstr2txt.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my $no = 0;
 my $clstr_no = "";

clstr2xml.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #usage: clstr_xml.pl [-len|-size] level1.clstr [level2.clstr level3.clstr ...]
 #purpose: to create xml file from cd-hit or hierarchical cd-hit(h-cd-hit) results

clstr_cut.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #keep only top $no proteins in cluster
 

clstr_merge.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 # the order of clusters need to be identical
 my ($master_clstr, @clstr) = @ARGV;

clstr_merge_noorder.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 # order of clusters don't need to be the same
 # but then I have to read everything into memory

clstr_quality_eval.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 ## calculate the sensitivity and specificity of clusters
 ## if the input fasta file has pre-defined classification term

clstr_quality_eval_by_link.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 ## calculate the sensitivity and specificity of clusters
 ## if the input fasta file has pre-defined classification term

clstr_reduce.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 
 $file90 = shift;

clstr_renumber.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 $no = 0;
 while($ll=<>){
   if ($ll =~ /^>Cluster (\d+)/) {

clstr_rep.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 $rep = "";
 $no = 0;

clstr_reps_faa_rev.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 # output single fasta file
 # for each cluster output at least $cutoff seqs
 

clstr_rev.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 # if nr90 from nr100 and
 #    nr80 from nr90, so I have nr90.clstr and nr80.clstr
 # but, in nr80.clstr, some gi numbers whose from nr100 are there

clstr_select.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #my $by = shift;
 my $min;

clstr_select_rep.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #my $by = shift;
 my $min;

clstr_size_histogram.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 if(@ARGV==0){
    print "Usage:\n\tclstr_size_histogram.pl [-bin N] clstr_file\n";

clstr_size_stat.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 if(@ARGV==0){
    print "Usage:\n\tclstr_size_stat.pl clstr_file\n";

clstr_sort_by.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my $sort_by_what = shift;
    $sort_by_what = "no" unless $sort_by_what;

clstr_sort_prot_by.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my $sort_by = shift;
    $sort_by = "len" unless ($sort_by);

clstr_sql_tbl.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 if(@ARGV==0){
   print "Usage:\n\tclstr_sql_tbl.pl clstr_file tbl_file\n";

clstr_sql_tbl_sort.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 if(@ARGV==0){
    print "Usage:\n\tclstr_sql_tbl_sort.pl table_file level\n";

make_multi_seq.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #note you have to use "-d 0" in the cd-hit run
 #note you better to use "-g 1" in the cd-hit run

plot_2d.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use Image::Magick;
 

plot_len1.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 $file90 = shift;
 $segs = shift;

psi-cd-hit/cd-hit-div.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #not like cd-hit-div, this script do not sort input
 #or throw away seq

psi-cd-hit/clstr_select_rep.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my $by = shift;
 my $min;

psi-cd-hit/clstr_select_seq.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my $by = shift;
 my $min;

psi-cd-hit/fetch_fasta_by_ids.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my ($gi_file, $seq_file) = @ARGV;
 

psi-cd-hit/fetch_fasta_exclude_ids.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my ($gi_file, $seq_file) = @ARGV;
 

psi-cd-hit/psi-2d.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 
 my $script_name = $0;

psi-cd-hit/psi-cd-hit-local.pl

@@ -1,7 +1,8 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 ################################################################################
 ######### PSI-cd-hit written by Weizhong Li at http://cd-hit.org
 ################################################################################
+use warnings;
 our $pid       = $$;
 our $db_in     = "";   ###################
 our $db_out    = "";   # input / output

psi-cd-hit/psi-cd-hit.pl

@@ -1,8 +1,10 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 ################################################################################
 ######### PSI-cd-hit written by Weizhong Li at http://cd-hit.org
 ################################################################################
 
+use warnings;
+
 our $script_name = $0;
 our $script_dir = $0;
    $script_dir =~ s/[^\/]+$//;